Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3hdq

2.360 Å

X-ray

2009-05-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-galactopyranose mutase
ID:Q9RYF1_DEIRA
AC:Q9RYF1
Organism:Deinococcus radiodurans
Reign:Bacteria
TaxID:243230
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:29.270
Number of residues:45
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.236705.375

% Hydrophobic% Polar
35.8964.11
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3hdqHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3hdq_1 Structure
HET Code: GDU
Formula: C15H22N2O17P2
Molecular weight: 564.286 g/mol
DrugBank ID: DB03501
Buried Surface Area:77 %
Polar Surface area: 316.82 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 7
Rings: 3
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 9

Mass center Coordinates

XYZ
24.1245-106.25973.4552
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3hdqRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C6'CGPRO- 843.810Hydrophobic
C6'CD1ILE- 863.790Hydrophobic
O6'NE2HIS- 1093.18152.11H-Bond
(Protein Donor)
N3OPHE- 1752.94153.72H-Bond
(Ligand Donor)
C1DCD1PHE- 1763.940Hydrophobic
C3DCE2TYR- 1793.90Hydrophobic
C2DCD2TYR- 1793.680Hydrophobic
C2DCBTHR- 1804.470Hydrophobic
O2DOG1THR- 1803162.8H-Bond
(Ligand Donor)
O3DNE1TRP- 1843.02144.17H-Bond
(Protein Donor)
C4DCG1VAL- 1954.030Hydrophobic
C1DCG2THR- 1964.280Hydrophobic
C5DCDARG- 1983.740Hydrophobic
O2ANEARG- 1982.87153.15H-Bond
(Protein Donor)
O2ANH2ARG- 1983.04140.45H-Bond
(Protein Donor)
O2ACZARG- 1983.370Ionic
(Protein Cationic)
C5DCG2VAL- 1994.340Hydrophobic
C4'CE2TYR- 2093.870Hydrophobic
C4'CZPHE- 2103.760Hydrophobic
O6'OG1THR- 2943.31154.68H-Bond
(Protein Donor)
O4ND2ASN- 2963.07152.6H-Bond
(Protein Donor)
O1BNH2ARG- 3053.3127.25H-Bond
(Protein Donor)
O3BNH2ARG- 3053.43133.32H-Bond
(Protein Donor)
O3BNH1ARG- 3052.85167.09H-Bond
(Protein Donor)
O1BCZARG- 3053.80Ionic
(Protein Cationic)
O1BOHTYR- 3352.83151.15H-Bond
(Protein Donor)
O2BOHTYR- 3702.77160.1H-Bond
(Protein Donor)
O6'OHOH- 4482.79144.77H-Bond
(Ligand Donor)
C1'C6FAD- 4503.770Hydrophobic
O4'O4FAD- 4502.8133.36H-Bond
(Ligand Donor)